Starting phenix.real_space_refine on Fri Mar 15 01:08:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dh9_27433/03_2024/8dh9_27433.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dh9_27433/03_2024/8dh9_27433.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dh9_27433/03_2024/8dh9_27433.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dh9_27433/03_2024/8dh9_27433.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dh9_27433/03_2024/8dh9_27433.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dh9_27433/03_2024/8dh9_27433.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 49 5.16 5 C 6557 2.51 5 N 1728 2.21 5 O 1895 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 805": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 761": "OD1" <-> "OD2" Residue "B TYR 805": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10229 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3994 Classifications: {'peptide': 495} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 464} Chain: "B" Number of atoms: 4025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 4025 Classifications: {'peptide': 499} Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 468} Chain: "C" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1087 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 6, 'TRANS': 134} Chain: "D" Number of atoms: 1123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1123 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 138} Time building chain proxies: 5.87, per 1000 atoms: 0.57 Number of scatterers: 10229 At special positions: 0 Unit cell: (141.96, 140.767, 159.854, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 49 16.00 O 1895 8.00 N 1728 7.00 C 6557 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 410 " distance=2.03 Simple disulfide: pdb=" SG CYS A 411 " - pdb=" SG CYS A 416 " distance=2.03 Simple disulfide: pdb=" SG CYS A 434 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 526 " distance=2.03 Simple disulfide: pdb=" SG CYS A 486 " - pdb=" SG CYS A 496 " distance=2.03 Simple disulfide: pdb=" SG CYS A 602 " - pdb=" SG CYS A 672 " distance=2.03 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 410 " distance=2.03 Simple disulfide: pdb=" SG CYS B 411 " - pdb=" SG CYS B 416 " distance=2.03 Simple disulfide: pdb=" SG CYS B 434 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS B 526 " distance=2.03 Simple disulfide: pdb=" SG CYS B 486 " - pdb=" SG CYS B 496 " distance=2.04 Simple disulfide: pdb=" SG CYS B 602 " - pdb=" SG CYS B 672 " distance=2.03 Simple disulfide: pdb=" SG CYS D 117 " - pdb=" SG CYS D 167 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.62 Conformation dependent library (CDL) restraints added in 1.8 seconds 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2458 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 26 sheets defined 20.3% alpha, 33.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 375 through 377 No H-bonds generated for 'chain 'A' and resid 375 through 377' Processing helix chain 'A' and resid 449 through 453 Processing helix chain 'A' and resid 528 through 533 removed outlier: 3.712A pdb=" N VAL A 533 " --> pdb=" O ASP A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 564 Processing helix chain 'A' and resid 731 through 735 removed outlier: 3.921A pdb=" N LYS A 735 " --> pdb=" O TRP A 731 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 731 through 735' Processing helix chain 'B' and resid 360 through 362 No H-bonds generated for 'chain 'B' and resid 360 through 362' Processing helix chain 'B' and resid 375 through 377 No H-bonds generated for 'chain 'B' and resid 375 through 377' Processing helix chain 'B' and resid 451 through 455 removed outlier: 3.559A pdb=" N SER B 454 " --> pdb=" O THR B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 532 removed outlier: 3.672A pdb=" N VAL B 532 " --> pdb=" O PRO B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 736 Processing helix chain 'C' and resid 2 through 26 Processing helix chain 'C' and resid 27 through 29 No H-bonds generated for 'chain 'C' and resid 27 through 29' Processing helix chain 'C' and resid 50 through 67 Processing helix chain 'C' and resid 70 through 94 Processing helix chain 'C' and resid 107 through 117 removed outlier: 3.843A pdb=" N ASP C 111 " --> pdb=" O PRO C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 141 removed outlier: 4.083A pdb=" N ASP C 141 " --> pdb=" O LEU C 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 49 removed outlier: 3.543A pdb=" N THR D 48 " --> pdb=" O ASP D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 88 Processing helix chain 'D' and resid 91 through 115 Processing helix chain 'D' and resid 129 through 138 removed outlier: 4.183A pdb=" N GLY D 133 " --> pdb=" O GLU D 129 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU D 136 " --> pdb=" O ASP D 132 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA D 137 " --> pdb=" O GLY D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 163 Processing sheet with id=AA1, first strand: chain 'A' and resid 337 through 339 Processing sheet with id=AA2, first strand: chain 'A' and resid 346 through 350 removed outlier: 3.548A pdb=" N ALA A 346 " --> pdb=" O PHE A 391 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 389 " --> pdb=" O PHE A 348 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER A 387 " --> pdb=" O CYS A 350 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 353 through 354 Processing sheet with id=AA4, first strand: chain 'A' and resid 372 through 373 removed outlier: 3.511A pdb=" N GLU A 372 " --> pdb=" O ARG A 368 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 433 through 436 Processing sheet with id=AA6, first strand: chain 'A' and resid 482 through 484 removed outlier: 4.247A pdb=" N LEU A 462 " --> pdb=" O LYS A 484 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 482 through 484 removed outlier: 4.247A pdb=" N LEU A 462 " --> pdb=" O LYS A 484 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 539 through 545 removed outlier: 4.020A pdb=" N VAL A 541 " --> pdb=" O SER A 555 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N SER A 555 " --> pdb=" O VAL A 541 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ALA A 543 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LYS A 553 " --> pdb=" O ALA A 543 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE A 545 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N LEU A 551 " --> pdb=" O ILE A 545 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 582 through 586 removed outlier: 3.826A pdb=" N PHE A 568 " --> pdb=" O VAL A 586 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 643 through 648 removed outlier: 3.532A pdb=" N ASP A 648 " --> pdb=" O ASN A 657 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 688 through 694 removed outlier: 5.609A pdb=" N TYR A 677 " --> pdb=" O VAL A 693 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 739 through 746 Processing sheet with id=AB4, first strand: chain 'A' and resid 781 through 787 Processing sheet with id=AB5, first strand: chain 'B' and resid 331 through 333 Processing sheet with id=AB6, first strand: chain 'B' and resid 331 through 333 removed outlier: 3.548A pdb=" N VAL B 389 " --> pdb=" O PHE B 348 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER B 387 " --> pdb=" O CYS B 350 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 337 through 341 Processing sheet with id=AB8, first strand: chain 'B' and resid 337 through 341 Processing sheet with id=AB9, first strand: chain 'B' and resid 432 through 436 removed outlier: 3.576A pdb=" N CYS B 496 " --> pdb=" O CYS B 445 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TRP B 447 " --> pdb=" O TYR B 494 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 482 through 484 removed outlier: 3.671A pdb=" N LEU B 462 " --> pdb=" O LYS B 484 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 482 through 484 removed outlier: 3.671A pdb=" N LEU B 462 " --> pdb=" O LYS B 484 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR B 507 " --> pdb=" O VAL B 527 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET B 509 " --> pdb=" O THR B 525 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 539 through 545 removed outlier: 5.966A pdb=" N ASN B 540 " --> pdb=" O GLU B 557 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLU B 557 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 596 " --> pdb=" O LEU B 552 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 582 through 586 removed outlier: 3.501A pdb=" N VAL B 607 " --> pdb=" O ALA B 627 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 643 through 648 Processing sheet with id=AC6, first strand: chain 'B' and resid 688 through 694 removed outlier: 5.733A pdb=" N TYR B 677 " --> pdb=" O VAL B 693 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 743 through 748 removed outlier: 6.260A pdb=" N CYS B 751 " --> pdb=" O LEU B 747 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 782 through 787 removed outlier: 3.524A pdb=" N TYR B 767 " --> pdb=" O VAL B 812 " (cutoff:3.500A) 462 hydrogen bonds defined for protein. 1224 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.51 Time building geometry restraints manager: 4.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3245 1.34 - 1.46: 2478 1.46 - 1.58: 4692 1.58 - 1.70: 0 1.70 - 1.82: 67 Bond restraints: 10482 Sorted by residual: bond pdb=" C TRP B 662 " pdb=" N LYS B 663 " ideal model delta sigma weight residual 1.327 1.342 -0.015 1.39e-02 5.18e+03 1.19e+00 bond pdb=" CA SER B 450 " pdb=" C SER B 450 " ideal model delta sigma weight residual 1.523 1.538 -0.015 1.34e-02 5.57e+03 1.18e+00 bond pdb=" N ASN B 393 " pdb=" CA ASN B 393 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.16e+00 bond pdb=" CA ILE D 69 " pdb=" CB ILE D 69 " ideal model delta sigma weight residual 1.539 1.527 0.012 1.18e-02 7.18e+03 1.10e+00 bond pdb=" CB LYS C 15 " pdb=" CG LYS C 15 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.94e-01 ... (remaining 10477 not shown) Histogram of bond angle deviations from ideal: 99.67 - 106.54: 356 106.54 - 113.41: 5933 113.41 - 120.29: 3408 120.29 - 127.16: 4426 127.16 - 134.03: 154 Bond angle restraints: 14277 Sorted by residual: angle pdb=" C SER A 481 " pdb=" N GLU A 482 " pdb=" CA GLU A 482 " ideal model delta sigma weight residual 122.74 113.82 8.92 2.44e+00 1.68e-01 1.34e+01 angle pdb=" CA LEU A 440 " pdb=" CB LEU A 440 " pdb=" CG LEU A 440 " ideal model delta sigma weight residual 116.30 128.86 -12.56 3.50e+00 8.16e-02 1.29e+01 angle pdb=" CA SER B 450 " pdb=" C SER B 450 " pdb=" N THR B 451 " ideal model delta sigma weight residual 116.84 122.89 -6.05 1.71e+00 3.42e-01 1.25e+01 angle pdb=" CB MET A 781 " pdb=" CG MET A 781 " pdb=" SD MET A 781 " ideal model delta sigma weight residual 112.70 102.51 10.19 3.00e+00 1.11e-01 1.15e+01 angle pdb=" N SER D 138 " pdb=" CA SER D 138 " pdb=" C SER D 138 " ideal model delta sigma weight residual 107.32 112.20 -4.88 1.65e+00 3.67e-01 8.75e+00 ... (remaining 14272 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 5919 17.64 - 35.28: 356 35.28 - 52.92: 52 52.92 - 70.56: 13 70.56 - 88.20: 11 Dihedral angle restraints: 6351 sinusoidal: 2566 harmonic: 3785 Sorted by residual: dihedral pdb=" CB CYS B 486 " pdb=" SG CYS B 486 " pdb=" SG CYS B 496 " pdb=" CB CYS B 496 " ideal model delta sinusoidal sigma weight residual 93.00 53.71 39.29 1 1.00e+01 1.00e-02 2.17e+01 dihedral pdb=" CB CYS D 117 " pdb=" SG CYS D 117 " pdb=" SG CYS D 167 " pdb=" CB CYS D 167 " ideal model delta sinusoidal sigma weight residual 93.00 60.65 32.35 1 1.00e+01 1.00e-02 1.49e+01 dihedral pdb=" CB CYS A 350 " pdb=" SG CYS A 350 " pdb=" SG CYS A 410 " pdb=" CB CYS A 410 " ideal model delta sinusoidal sigma weight residual 93.00 62.06 30.94 1 1.00e+01 1.00e-02 1.37e+01 ... (remaining 6348 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 979 0.029 - 0.058: 413 0.058 - 0.086: 117 0.086 - 0.115: 107 0.115 - 0.144: 20 Chirality restraints: 1636 Sorted by residual: chirality pdb=" CG LEU A 462 " pdb=" CB LEU A 462 " pdb=" CD1 LEU A 462 " pdb=" CD2 LEU A 462 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA ILE B 770 " pdb=" N ILE B 770 " pdb=" C ILE B 770 " pdb=" CB ILE B 770 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CA ILE A 511 " pdb=" N ILE A 511 " pdb=" C ILE A 511 " pdb=" CB ILE A 511 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 ... (remaining 1633 not shown) Planarity restraints: 1792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 374 " 0.031 5.00e-02 4.00e+02 4.71e-02 3.56e+00 pdb=" N PRO A 375 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 375 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 375 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 558 " 0.029 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO B 559 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 559 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 559 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 756 " -0.011 2.00e-02 2.50e+03 9.13e-03 2.08e+00 pdb=" CG TRP A 756 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP A 756 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP A 756 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 756 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 756 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 756 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 756 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 756 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 756 " 0.000 2.00e-02 2.50e+03 ... (remaining 1789 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 168 2.64 - 3.20: 9241 3.20 - 3.77: 16241 3.77 - 4.33: 21882 4.33 - 4.90: 34808 Nonbonded interactions: 82340 Sorted by model distance: nonbonded pdb=" OG SER B 721 " pdb=" OD1 ASN B 724 " model vdw 2.073 2.440 nonbonded pdb=" OE1 GLU B 422 " pdb=" OH TYR B 424 " model vdw 2.203 2.440 nonbonded pdb=" OG SER A 721 " pdb=" OD1 ASN A 724 " model vdw 2.211 2.440 nonbonded pdb=" O ASN D 43 " pdb=" ND1 HIS D 47 " model vdw 2.217 2.520 nonbonded pdb=" OG SER D 91 " pdb=" OD1 ASN D 93 " model vdw 2.244 2.440 ... (remaining 82335 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 332 through 826) } ncs_group { reference = chain 'C' selection = (chain 'D' and resid 22 through 162) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.060 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 28.960 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5385 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10482 Z= 0.170 Angle : 0.649 12.562 14277 Z= 0.355 Chirality : 0.042 0.144 1636 Planarity : 0.004 0.047 1792 Dihedral : 12.032 88.201 3854 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.83 % Favored : 96.94 % Rotamer: Outliers : 0.08 % Allowed : 0.08 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.24), residues: 1273 helix: 1.25 (0.35), residues: 212 sheet: 0.06 (0.23), residues: 457 loop : 0.20 (0.27), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 756 HIS 0.004 0.001 HIS B 465 PHE 0.014 0.001 PHE B 334 TYR 0.016 0.001 TYR A 424 ARG 0.003 0.000 ARG A 639 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 372 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 348 PHE cc_start: 0.6781 (m-80) cc_final: 0.6130 (m-80) REVERT: A 391 PHE cc_start: 0.6449 (m-80) cc_final: 0.6179 (m-80) REVERT: A 393 ASN cc_start: 0.7221 (t0) cc_final: 0.6902 (p0) REVERT: A 494 TYR cc_start: 0.5411 (m-80) cc_final: 0.4828 (m-10) REVERT: A 509 MET cc_start: 0.6869 (tpt) cc_final: 0.6275 (tpt) REVERT: A 510 TRP cc_start: 0.7177 (p90) cc_final: 0.5651 (p90) REVERT: A 580 GLN cc_start: 0.8292 (mm-40) cc_final: 0.7975 (mp10) REVERT: A 693 VAL cc_start: 0.7702 (t) cc_final: 0.7354 (p) REVERT: A 768 LEU cc_start: 0.7151 (mt) cc_final: 0.6807 (mt) REVERT: A 783 TRP cc_start: 0.7237 (p-90) cc_final: 0.7009 (p-90) REVERT: B 428 VAL cc_start: 0.5939 (m) cc_final: 0.5708 (m) REVERT: B 429 ASN cc_start: 0.6673 (t0) cc_final: 0.6032 (t0) REVERT: B 484 LYS cc_start: 0.7770 (tptt) cc_final: 0.7400 (mtpp) REVERT: B 507 TYR cc_start: 0.6530 (m-10) cc_final: 0.6220 (m-10) REVERT: B 530 ASP cc_start: 0.8091 (m-30) cc_final: 0.7878 (m-30) REVERT: B 554 VAL cc_start: 0.7587 (t) cc_final: 0.7292 (m) REVERT: B 555 SER cc_start: 0.7074 (p) cc_final: 0.6858 (t) REVERT: B 582 LYS cc_start: 0.7572 (mttt) cc_final: 0.7095 (tptp) REVERT: B 612 ARG cc_start: 0.5827 (ptt180) cc_final: 0.5515 (tmm-80) REVERT: B 628 TYR cc_start: 0.7351 (m-80) cc_final: 0.7048 (m-80) REVERT: B 647 MET cc_start: 0.6224 (mmm) cc_final: 0.5381 (tpp) REVERT: B 743 SER cc_start: 0.6406 (m) cc_final: 0.6154 (p) REVERT: B 795 ILE cc_start: 0.8543 (mt) cc_final: 0.7914 (mt) REVERT: B 814 MET cc_start: 0.4356 (mpp) cc_final: 0.3860 (mpp) REVERT: C 8 ASP cc_start: 0.7854 (p0) cc_final: 0.7354 (p0) REVERT: C 9 ASP cc_start: 0.8356 (m-30) cc_final: 0.7865 (m-30) REVERT: C 11 LYS cc_start: 0.8654 (mtmm) cc_final: 0.7755 (mtmm) REVERT: C 54 MET cc_start: 0.8751 (mtm) cc_final: 0.7903 (mmp) REVERT: C 65 LEU cc_start: 0.8262 (mt) cc_final: 0.8011 (mt) REVERT: C 84 ARG cc_start: 0.7995 (mtp180) cc_final: 0.7215 (ttm-80) REVERT: C 85 ASP cc_start: 0.8360 (m-30) cc_final: 0.7931 (m-30) REVERT: C 86 LEU cc_start: 0.8799 (mm) cc_final: 0.8594 (mm) REVERT: C 88 HIS cc_start: 0.7906 (m90) cc_final: 0.7301 (m90) REVERT: D 153 SER cc_start: 0.6061 (m) cc_final: 0.5734 (p) REVERT: D 160 GLN cc_start: 0.7560 (mm-40) cc_final: 0.7178 (tp-100) outliers start: 1 outliers final: 0 residues processed: 373 average time/residue: 0.2381 time to fit residues: 119.4694 Evaluate side-chains 288 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 288 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN A 796 HIS ** B 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN ** B 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 681 HIS B 685 HIS ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5856 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 10482 Z= 0.375 Angle : 0.829 10.103 14277 Z= 0.447 Chirality : 0.049 0.207 1636 Planarity : 0.007 0.067 1792 Dihedral : 5.838 21.712 1382 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 22.36 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.16 % Favored : 95.44 % Rotamer: Outliers : 0.93 % Allowed : 5.58 % Favored : 93.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.23), residues: 1273 helix: 0.43 (0.34), residues: 215 sheet: -0.12 (0.23), residues: 468 loop : -0.38 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP A 731 HIS 0.016 0.003 HIS B 584 PHE 0.045 0.003 PHE B 568 TYR 0.038 0.003 TYR B 405 ARG 0.009 0.001 ARG B 612 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 330 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 ILE cc_start: 0.7726 (mp) cc_final: 0.7391 (tp) REVERT: A 341 SER cc_start: 0.8202 (p) cc_final: 0.7891 (m) REVERT: A 369 ASN cc_start: 0.8853 (m-40) cc_final: 0.7704 (t0) REVERT: A 393 ASN cc_start: 0.7285 (t0) cc_final: 0.7013 (p0) REVERT: A 394 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7073 (pp) REVERT: A 413 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6893 (mp0) REVERT: A 447 TRP cc_start: 0.7705 (p-90) cc_final: 0.7348 (p-90) REVERT: A 448 SER cc_start: 0.8701 (p) cc_final: 0.8458 (t) REVERT: A 462 LEU cc_start: 0.6931 (mp) cc_final: 0.6729 (mp) REVERT: A 464 TYR cc_start: 0.6098 (p90) cc_final: 0.5749 (p90) REVERT: A 465 HIS cc_start: 0.6596 (t70) cc_final: 0.6374 (t-90) REVERT: A 478 HIS cc_start: 0.6883 (t-90) cc_final: 0.6658 (t-90) REVERT: A 480 THR cc_start: 0.6648 (m) cc_final: 0.6140 (m) REVERT: A 494 TYR cc_start: 0.5900 (m-80) cc_final: 0.5512 (m-80) REVERT: A 498 PHE cc_start: 0.7049 (t80) cc_final: 0.6464 (t80) REVERT: A 509 MET cc_start: 0.7255 (tpt) cc_final: 0.6820 (tpt) REVERT: A 510 TRP cc_start: 0.7181 (p90) cc_final: 0.5944 (p90) REVERT: A 512 ARG cc_start: 0.5557 (tpp80) cc_final: 0.4740 (tpp80) REVERT: A 539 SER cc_start: 0.7739 (p) cc_final: 0.7456 (t) REVERT: A 605 TYR cc_start: 0.7846 (m-80) cc_final: 0.7350 (m-80) REVERT: A 608 GLN cc_start: 0.5605 (mt0) cc_final: 0.4983 (mm-40) REVERT: A 613 ARG cc_start: 0.8182 (tpt90) cc_final: 0.7472 (tpt170) REVERT: A 617 LEU cc_start: 0.6150 (mt) cc_final: 0.5403 (pp) REVERT: A 681 HIS cc_start: 0.7766 (m-70) cc_final: 0.7358 (m-70) REVERT: A 685 HIS cc_start: 0.4693 (OUTLIER) cc_final: 0.3439 (t-170) REVERT: A 753 ILE cc_start: 0.7898 (mm) cc_final: 0.7657 (tp) REVERT: A 768 LEU cc_start: 0.7964 (mt) cc_final: 0.7519 (mt) REVERT: A 809 LEU cc_start: 0.8233 (tp) cc_final: 0.7107 (pp) REVERT: B 358 ILE cc_start: -0.6150 (OUTLIER) cc_final: -0.6846 (tp) REVERT: B 427 ASP cc_start: 0.5962 (t0) cc_final: 0.4990 (t0) REVERT: B 429 ASN cc_start: 0.7514 (t0) cc_final: 0.6722 (p0) REVERT: B 439 TYR cc_start: 0.7798 (m-10) cc_final: 0.7534 (m-10) REVERT: B 507 TYR cc_start: 0.6655 (m-10) cc_final: 0.6090 (m-10) REVERT: B 521 ASP cc_start: 0.6113 (m-30) cc_final: 0.5661 (p0) REVERT: B 530 ASP cc_start: 0.8162 (m-30) cc_final: 0.7958 (m-30) REVERT: B 572 TYR cc_start: 0.6907 (p90) cc_final: 0.6643 (p90) REVERT: B 638 MET cc_start: 0.5515 (ppp) cc_final: 0.5165 (ppp) REVERT: B 647 MET cc_start: 0.6486 (mmm) cc_final: 0.4823 (tmm) REVERT: B 701 PHE cc_start: 0.6519 (p90) cc_final: 0.6293 (p90) REVERT: B 771 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7267 (tp30) REVERT: B 782 LYS cc_start: 0.6998 (OUTLIER) cc_final: 0.6376 (pttm) REVERT: B 784 LEU cc_start: 0.7819 (mp) cc_final: 0.7375 (pt) REVERT: B 797 ASP cc_start: 0.5944 (t0) cc_final: 0.5601 (t70) REVERT: B 814 MET cc_start: 0.4949 (mpp) cc_final: 0.4465 (mpp) REVERT: C 13 LEU cc_start: 0.8147 (mt) cc_final: 0.7944 (mt) REVERT: C 53 LYS cc_start: 0.8173 (mtmt) cc_final: 0.7902 (mtmt) REVERT: C 54 MET cc_start: 0.8670 (mtm) cc_final: 0.8318 (mtt) REVERT: C 58 LEU cc_start: 0.8119 (mt) cc_final: 0.7840 (mt) REVERT: C 62 GLN cc_start: 0.8205 (tt0) cc_final: 0.7929 (tt0) REVERT: C 80 LEU cc_start: 0.8677 (tt) cc_final: 0.8442 (tt) REVERT: C 81 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7414 (mm-30) REVERT: C 84 ARG cc_start: 0.8386 (mtp180) cc_final: 0.7446 (ttm170) REVERT: C 85 ASP cc_start: 0.8657 (m-30) cc_final: 0.8290 (m-30) REVERT: C 87 LEU cc_start: 0.8828 (pp) cc_final: 0.8617 (pp) REVERT: C 88 HIS cc_start: 0.8243 (m90) cc_final: 0.7578 (m90) REVERT: C 111 ASP cc_start: 0.7937 (t0) cc_final: 0.7376 (m-30) REVERT: C 120 SER cc_start: 0.8954 (m) cc_final: 0.8718 (m) REVERT: D 160 GLN cc_start: 0.7617 (mm-40) cc_final: 0.7205 (tp40) outliers start: 11 outliers final: 3 residues processed: 337 average time/residue: 0.2439 time to fit residues: 112.7903 Evaluate side-chains 296 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 288 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 0.7980 chunk 35 optimal weight: 0.4980 chunk 95 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 31 optimal weight: 0.4980 chunk 114 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 796 HIS ** B 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 681 HIS D 28 GLN D 83 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5848 moved from start: 0.5073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10482 Z= 0.235 Angle : 0.684 10.897 14277 Z= 0.357 Chirality : 0.047 0.217 1636 Planarity : 0.005 0.055 1792 Dihedral : 5.357 28.011 1382 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.38 % Favored : 96.47 % Rotamer: Outliers : 0.17 % Allowed : 3.38 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.23), residues: 1273 helix: 0.44 (0.34), residues: 216 sheet: -0.03 (0.24), residues: 474 loop : -0.32 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 703 HIS 0.007 0.001 HIS B 584 PHE 0.013 0.001 PHE B 793 TYR 0.016 0.001 TYR A 379 ARG 0.010 0.001 ARG B 512 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 323 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 LYS cc_start: 0.7788 (mmtt) cc_final: 0.7240 (mmtp) REVERT: A 338 ILE cc_start: 0.7609 (mp) cc_final: 0.7170 (tp) REVERT: A 341 SER cc_start: 0.8126 (p) cc_final: 0.7847 (m) REVERT: A 370 LEU cc_start: 0.7979 (mt) cc_final: 0.7641 (mt) REVERT: A 393 ASN cc_start: 0.7159 (t0) cc_final: 0.6734 (p0) REVERT: A 419 ARG cc_start: 0.8105 (mtt180) cc_final: 0.7836 (mmt-90) REVERT: A 426 ILE cc_start: 0.7815 (mm) cc_final: 0.7467 (tp) REVERT: A 447 TRP cc_start: 0.7675 (p-90) cc_final: 0.7406 (p-90) REVERT: A 448 SER cc_start: 0.8787 (p) cc_final: 0.8410 (t) REVERT: A 480 THR cc_start: 0.6852 (m) cc_final: 0.6350 (m) REVERT: A 498 PHE cc_start: 0.6681 (t80) cc_final: 0.6396 (t80) REVERT: A 509 MET cc_start: 0.7150 (tpt) cc_final: 0.6828 (tpt) REVERT: A 510 TRP cc_start: 0.7197 (p90) cc_final: 0.5987 (p90) REVERT: A 533 VAL cc_start: 0.8225 (t) cc_final: 0.7934 (p) REVERT: A 605 TYR cc_start: 0.7924 (m-80) cc_final: 0.7490 (m-80) REVERT: A 613 ARG cc_start: 0.7954 (tpt90) cc_final: 0.7207 (tpt170) REVERT: A 617 LEU cc_start: 0.6167 (mt) cc_final: 0.5403 (pp) REVERT: A 681 HIS cc_start: 0.7638 (m-70) cc_final: 0.7401 (m-70) REVERT: A 753 ILE cc_start: 0.7903 (mm) cc_final: 0.7652 (tp) REVERT: A 767 TYR cc_start: 0.6780 (p90) cc_final: 0.6247 (p90) REVERT: B 512 ARG cc_start: 0.6082 (pmt-80) cc_final: 0.5799 (pmt-80) REVERT: B 545 ILE cc_start: 0.6227 (mp) cc_final: 0.5998 (mp) REVERT: B 565 ASN cc_start: 0.8206 (m-40) cc_final: 0.7545 (p0) REVERT: B 566 LEU cc_start: 0.8565 (pt) cc_final: 0.8260 (pt) REVERT: B 567 GLN cc_start: 0.7547 (tm-30) cc_final: 0.7174 (tm-30) REVERT: B 614 LEU cc_start: 0.8714 (tt) cc_final: 0.8423 (tp) REVERT: B 647 MET cc_start: 0.6563 (mmm) cc_final: 0.4760 (tmm) REVERT: B 754 LEU cc_start: 0.7811 (tp) cc_final: 0.7603 (tp) REVERT: B 755 SER cc_start: 0.7408 (m) cc_final: 0.6934 (p) REVERT: B 771 GLU cc_start: 0.7391 (tm-30) cc_final: 0.7123 (tp30) REVERT: B 782 LYS cc_start: 0.7709 (mtmm) cc_final: 0.6807 (pttm) REVERT: B 784 LEU cc_start: 0.7819 (mp) cc_final: 0.7310 (pt) REVERT: B 814 MET cc_start: 0.4821 (mpp) cc_final: 0.4391 (mpp) REVERT: C 13 LEU cc_start: 0.8173 (mt) cc_final: 0.7945 (mt) REVERT: C 54 MET cc_start: 0.8656 (mtm) cc_final: 0.8074 (mmp) REVERT: C 61 TYR cc_start: 0.8537 (m-80) cc_final: 0.8048 (m-80) REVERT: C 62 GLN cc_start: 0.8111 (tt0) cc_final: 0.7778 (tt0) REVERT: C 65 LEU cc_start: 0.8665 (mt) cc_final: 0.8442 (mt) REVERT: C 75 GLN cc_start: 0.8184 (pp30) cc_final: 0.7891 (tp40) REVERT: C 81 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7245 (mm-30) REVERT: C 84 ARG cc_start: 0.8353 (mtp180) cc_final: 0.7418 (ttm-80) REVERT: C 85 ASP cc_start: 0.8566 (m-30) cc_final: 0.8185 (m-30) REVERT: C 87 LEU cc_start: 0.8758 (pp) cc_final: 0.8554 (pp) REVERT: C 88 HIS cc_start: 0.8091 (m90) cc_final: 0.7547 (m90) REVERT: C 111 ASP cc_start: 0.7882 (t0) cc_final: 0.7351 (m-30) REVERT: C 117 SER cc_start: 0.7904 (t) cc_final: 0.7527 (m) REVERT: C 120 SER cc_start: 0.8942 (m) cc_final: 0.8637 (p) REVERT: D 160 GLN cc_start: 0.7540 (mm-40) cc_final: 0.7038 (tp40) outliers start: 2 outliers final: 0 residues processed: 323 average time/residue: 0.2679 time to fit residues: 119.9590 Evaluate side-chains 290 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 12 optimal weight: 0.0020 chunk 54 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 115 optimal weight: 0.0770 chunk 121 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.4746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 796 HIS B 418 HIS B 431 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5835 moved from start: 0.5556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10482 Z= 0.188 Angle : 0.637 9.675 14277 Z= 0.330 Chirality : 0.045 0.183 1636 Planarity : 0.005 0.056 1792 Dihedral : 5.125 25.676 1382 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.85 % Favored : 96.07 % Rotamer: Outliers : 0.08 % Allowed : 3.47 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.24), residues: 1273 helix: 0.68 (0.35), residues: 216 sheet: -0.06 (0.23), residues: 483 loop : -0.35 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 447 HIS 0.004 0.001 HIS B 685 PHE 0.027 0.002 PHE B 568 TYR 0.017 0.002 TYR B 405 ARG 0.011 0.001 ARG A 612 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 313 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 LYS cc_start: 0.7763 (mmtt) cc_final: 0.7289 (mmtp) REVERT: A 338 ILE cc_start: 0.7509 (mp) cc_final: 0.7156 (tp) REVERT: A 365 VAL cc_start: 0.7662 (t) cc_final: 0.7294 (m) REVERT: A 373 LYS cc_start: 0.8274 (tmtt) cc_final: 0.7951 (tmtt) REVERT: A 393 ASN cc_start: 0.7111 (t0) cc_final: 0.6665 (p0) REVERT: A 443 MET cc_start: 0.5800 (ppp) cc_final: 0.4888 (tmm) REVERT: A 464 TYR cc_start: 0.6274 (p90) cc_final: 0.5677 (p90) REVERT: A 494 TYR cc_start: 0.5817 (m-80) cc_final: 0.5466 (m-80) REVERT: A 498 PHE cc_start: 0.6789 (t80) cc_final: 0.6389 (t80) REVERT: A 510 TRP cc_start: 0.7278 (p90) cc_final: 0.6005 (p90) REVERT: A 511 ILE cc_start: 0.7486 (mm) cc_final: 0.6970 (mm) REVERT: A 533 VAL cc_start: 0.8255 (t) cc_final: 0.8033 (p) REVERT: A 577 LYS cc_start: 0.8480 (mptt) cc_final: 0.8246 (mmtm) REVERT: A 605 TYR cc_start: 0.7941 (m-80) cc_final: 0.7661 (m-80) REVERT: A 681 HIS cc_start: 0.7649 (m-70) cc_final: 0.7408 (m-70) REVERT: A 725 PHE cc_start: 0.6279 (m-80) cc_final: 0.6071 (m-80) REVERT: A 753 ILE cc_start: 0.7867 (mm) cc_final: 0.7579 (tp) REVERT: A 767 TYR cc_start: 0.6664 (p90) cc_final: 0.6206 (p90) REVERT: B 502 PHE cc_start: 0.5789 (m-80) cc_final: 0.5302 (m-10) REVERT: B 512 ARG cc_start: 0.6247 (pmt-80) cc_final: 0.5949 (pmt-80) REVERT: B 554 VAL cc_start: 0.7562 (t) cc_final: 0.7204 (t) REVERT: B 555 SER cc_start: 0.6494 (t) cc_final: 0.6191 (m) REVERT: B 556 TRP cc_start: 0.6897 (p90) cc_final: 0.6325 (p90) REVERT: B 566 LEU cc_start: 0.8711 (pt) cc_final: 0.8240 (pt) REVERT: B 580 GLN cc_start: 0.8007 (pm20) cc_final: 0.7744 (pm20) REVERT: B 647 MET cc_start: 0.6539 (mmm) cc_final: 0.4738 (tmm) REVERT: B 701 PHE cc_start: 0.5856 (p90) cc_final: 0.5591 (p90) REVERT: B 755 SER cc_start: 0.7479 (m) cc_final: 0.7027 (p) REVERT: B 771 GLU cc_start: 0.7324 (tm-30) cc_final: 0.7083 (tp30) REVERT: B 782 LYS cc_start: 0.7576 (mtmm) cc_final: 0.7012 (mtmm) REVERT: B 814 MET cc_start: 0.4635 (mpp) cc_final: 0.4244 (mpp) REVERT: C 8 ASP cc_start: 0.8086 (p0) cc_final: 0.7508 (p0) REVERT: C 11 LYS cc_start: 0.8645 (mtmm) cc_final: 0.8060 (mtmm) REVERT: C 13 LEU cc_start: 0.8127 (mt) cc_final: 0.7918 (mt) REVERT: C 53 LYS cc_start: 0.8303 (mtmt) cc_final: 0.7898 (ptmm) REVERT: C 54 MET cc_start: 0.8752 (mtm) cc_final: 0.7908 (mtt) REVERT: C 61 TYR cc_start: 0.8558 (m-80) cc_final: 0.7996 (m-80) REVERT: C 62 GLN cc_start: 0.8124 (tt0) cc_final: 0.7593 (tt0) REVERT: C 65 LEU cc_start: 0.8620 (mt) cc_final: 0.8389 (mt) REVERT: C 81 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7237 (mm-30) REVERT: C 84 ARG cc_start: 0.8363 (mtp180) cc_final: 0.7365 (ttm170) REVERT: C 85 ASP cc_start: 0.8496 (m-30) cc_final: 0.8116 (m-30) REVERT: C 88 HIS cc_start: 0.8049 (m90) cc_final: 0.7523 (m90) REVERT: C 111 ASP cc_start: 0.7902 (t0) cc_final: 0.7358 (m-30) REVERT: C 117 SER cc_start: 0.7808 (t) cc_final: 0.7433 (m) REVERT: C 120 SER cc_start: 0.8950 (m) cc_final: 0.8618 (p) REVERT: C 134 GLN cc_start: 0.8327 (mp10) cc_final: 0.8091 (mp10) REVERT: D 160 GLN cc_start: 0.7541 (mm-40) cc_final: 0.7152 (tp40) outliers start: 1 outliers final: 0 residues processed: 313 average time/residue: 0.2443 time to fit residues: 104.7897 Evaluate side-chains 279 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 84 optimal weight: 5.9990 chunk 0 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 567 GLN A 569 GLN A 724 ASN ** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN ** B 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6021 moved from start: 0.6815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 10482 Z= 0.342 Angle : 0.771 13.975 14277 Z= 0.414 Chirality : 0.047 0.178 1636 Planarity : 0.006 0.056 1792 Dihedral : 6.017 26.314 1382 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 23.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.18 % Favored : 94.74 % Rotamer: Outliers : 0.08 % Allowed : 4.14 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.23), residues: 1273 helix: -0.13 (0.33), residues: 222 sheet: -0.59 (0.23), residues: 469 loop : -0.72 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 703 HIS 0.008 0.002 HIS B 685 PHE 0.022 0.003 PHE C 41 TYR 0.016 0.002 TYR B 379 ARG 0.014 0.001 ARG A 400 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 308 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 LYS cc_start: 0.7960 (mmtt) cc_final: 0.7500 (mmtp) REVERT: A 338 ILE cc_start: 0.7809 (mp) cc_final: 0.7320 (tp) REVERT: A 373 LYS cc_start: 0.8441 (tmtt) cc_final: 0.8190 (tptp) REVERT: A 393 ASN cc_start: 0.6874 (t0) cc_final: 0.6334 (p0) REVERT: A 426 ILE cc_start: 0.8102 (mm) cc_final: 0.7875 (tp) REVERT: A 464 TYR cc_start: 0.6601 (p90) cc_final: 0.5867 (p90) REVERT: A 489 GLN cc_start: 0.7576 (mp10) cc_final: 0.7033 (mp10) REVERT: A 494 TYR cc_start: 0.5957 (m-80) cc_final: 0.5151 (m-80) REVERT: A 497 VAL cc_start: 0.7918 (p) cc_final: 0.6956 (m) REVERT: A 498 PHE cc_start: 0.6598 (t80) cc_final: 0.6369 (t80) REVERT: A 510 TRP cc_start: 0.7502 (p90) cc_final: 0.7170 (p90) REVERT: A 515 HIS cc_start: 0.5950 (t70) cc_final: 0.5094 (t70) REVERT: A 533 VAL cc_start: 0.8360 (t) cc_final: 0.8124 (p) REVERT: A 577 LYS cc_start: 0.8467 (mptt) cc_final: 0.8112 (mmtm) REVERT: A 605 TYR cc_start: 0.8134 (m-80) cc_final: 0.7902 (m-80) REVERT: A 632 MET cc_start: 0.1219 (mmm) cc_final: 0.0351 (mmm) REVERT: A 655 GLU cc_start: 0.7247 (mt-10) cc_final: 0.6620 (pp20) REVERT: A 683 THR cc_start: 0.5757 (p) cc_final: 0.4836 (m) REVERT: A 725 PHE cc_start: 0.6637 (m-80) cc_final: 0.6408 (m-80) REVERT: A 753 ILE cc_start: 0.8074 (mm) cc_final: 0.7788 (tp) REVERT: A 767 TYR cc_start: 0.7019 (p90) cc_final: 0.6605 (p90) REVERT: B 493 PHE cc_start: 0.8175 (m-10) cc_final: 0.7970 (m-80) REVERT: B 521 ASP cc_start: 0.6997 (p0) cc_final: 0.6530 (m-30) REVERT: B 556 TRP cc_start: 0.7006 (p90) cc_final: 0.6693 (p90) REVERT: B 582 LYS cc_start: 0.7753 (mmpt) cc_final: 0.7480 (mmtm) REVERT: B 647 MET cc_start: 0.6596 (mmm) cc_final: 0.4858 (tmm) REVERT: B 771 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7293 (tp30) REVERT: B 777 GLU cc_start: 0.7486 (mp0) cc_final: 0.7181 (mp0) REVERT: B 782 LYS cc_start: 0.7752 (mtmm) cc_final: 0.7156 (mtmm) REVERT: B 794 TYR cc_start: 0.7401 (m-80) cc_final: 0.7010 (m-80) REVERT: B 814 MET cc_start: 0.5046 (mpp) cc_final: 0.4659 (mpp) REVERT: C 8 ASP cc_start: 0.8077 (p0) cc_final: 0.7737 (p0) REVERT: C 11 LYS cc_start: 0.8727 (mtmm) cc_final: 0.8292 (mtmm) REVERT: C 13 LEU cc_start: 0.8196 (mt) cc_final: 0.7986 (mt) REVERT: C 53 LYS cc_start: 0.8419 (mtmt) cc_final: 0.8069 (pttt) REVERT: C 54 MET cc_start: 0.8702 (mtm) cc_final: 0.8202 (mtt) REVERT: C 58 LEU cc_start: 0.8389 (mt) cc_final: 0.8113 (mt) REVERT: C 62 GLN cc_start: 0.8377 (tt0) cc_final: 0.8005 (tt0) REVERT: C 81 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7576 (mm-30) REVERT: C 82 ASN cc_start: 0.8032 (m110) cc_final: 0.7815 (m110) REVERT: C 84 ARG cc_start: 0.8551 (mtp180) cc_final: 0.7466 (ttm170) REVERT: C 85 ASP cc_start: 0.8631 (m-30) cc_final: 0.8276 (m-30) REVERT: C 88 HIS cc_start: 0.8139 (m90) cc_final: 0.7605 (m90) REVERT: C 120 SER cc_start: 0.8977 (m) cc_final: 0.8726 (p) REVERT: C 135 ASP cc_start: 0.8635 (m-30) cc_final: 0.7992 (m-30) REVERT: C 138 GLN cc_start: 0.9078 (mm-40) cc_final: 0.8558 (pp30) REVERT: C 139 GLN cc_start: 0.8504 (tm-30) cc_final: 0.8127 (tm-30) REVERT: D 160 GLN cc_start: 0.7487 (mm-40) cc_final: 0.7048 (mm-40) outliers start: 1 outliers final: 0 residues processed: 309 average time/residue: 0.2281 time to fit residues: 96.6844 Evaluate side-chains 272 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 272 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 24 optimal weight: 0.0980 chunk 71 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 chunk 101 optimal weight: 0.0670 chunk 56 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN A 569 GLN B 349 HIS B 431 ASN ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5949 moved from start: 0.7105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10482 Z= 0.200 Angle : 0.661 10.878 14277 Z= 0.343 Chirality : 0.047 0.441 1636 Planarity : 0.005 0.057 1792 Dihedral : 5.411 28.557 1382 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.24 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.23), residues: 1273 helix: 0.39 (0.34), residues: 222 sheet: -0.41 (0.24), residues: 469 loop : -0.69 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 447 HIS 0.004 0.001 HIS B 685 PHE 0.024 0.002 PHE C 92 TYR 0.015 0.001 TYR A 572 ARG 0.006 0.001 ARG D 105 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 303 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 LYS cc_start: 0.7770 (mmtt) cc_final: 0.7336 (mmtp) REVERT: A 338 ILE cc_start: 0.7605 (mp) cc_final: 0.7206 (tp) REVERT: A 393 ASN cc_start: 0.6732 (t0) cc_final: 0.6452 (t0) REVERT: A 426 ILE cc_start: 0.8022 (mm) cc_final: 0.7640 (tp) REVERT: A 464 TYR cc_start: 0.6637 (p90) cc_final: 0.5698 (p90) REVERT: A 480 THR cc_start: 0.6834 (m) cc_final: 0.6404 (m) REVERT: A 489 GLN cc_start: 0.7725 (mp10) cc_final: 0.7362 (mp10) REVERT: A 498 PHE cc_start: 0.6394 (t80) cc_final: 0.6145 (t80) REVERT: A 510 TRP cc_start: 0.7571 (p90) cc_final: 0.6997 (p90) REVERT: A 511 ILE cc_start: 0.7962 (tp) cc_final: 0.7681 (mm) REVERT: A 577 LYS cc_start: 0.8318 (mptt) cc_final: 0.7977 (mptt) REVERT: A 605 TYR cc_start: 0.8034 (m-80) cc_final: 0.7769 (m-10) REVERT: A 632 MET cc_start: 0.0873 (mmm) cc_final: 0.0019 (mmm) REVERT: A 655 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6390 (pp20) REVERT: A 725 PHE cc_start: 0.6559 (m-80) cc_final: 0.6295 (m-80) REVERT: A 753 ILE cc_start: 0.7928 (mm) cc_final: 0.7678 (tp) REVERT: A 767 TYR cc_start: 0.6873 (p90) cc_final: 0.6422 (p90) REVERT: B 503 LEU cc_start: 0.7884 (mm) cc_final: 0.7654 (mm) REVERT: B 521 ASP cc_start: 0.6961 (p0) cc_final: 0.6507 (m-30) REVERT: B 613 ARG cc_start: 0.6920 (ttt90) cc_final: 0.6585 (mtt-85) REVERT: B 647 MET cc_start: 0.6575 (mmm) cc_final: 0.4821 (tmm) REVERT: B 755 SER cc_start: 0.7783 (m) cc_final: 0.7305 (p) REVERT: B 761 ASP cc_start: 0.6168 (t0) cc_final: 0.5787 (t70) REVERT: B 771 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7225 (tp30) REVERT: B 782 LYS cc_start: 0.7638 (mtmm) cc_final: 0.7016 (mtmm) REVERT: B 794 TYR cc_start: 0.7322 (m-80) cc_final: 0.6998 (m-80) REVERT: B 814 MET cc_start: 0.4821 (mpp) cc_final: 0.4520 (mpp) REVERT: B 819 LYS cc_start: 0.7249 (tmtt) cc_final: 0.6302 (mtpt) REVERT: C 54 MET cc_start: 0.8697 (mtm) cc_final: 0.8199 (mtt) REVERT: C 61 TYR cc_start: 0.8678 (m-80) cc_final: 0.7982 (m-80) REVERT: C 62 GLN cc_start: 0.8328 (tt0) cc_final: 0.7787 (tt0) REVERT: C 65 LEU cc_start: 0.8649 (mt) cc_final: 0.8443 (mt) REVERT: C 81 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7503 (mm-30) REVERT: C 84 ARG cc_start: 0.8494 (mtp180) cc_final: 0.7528 (ttm170) REVERT: C 85 ASP cc_start: 0.8603 (m-30) cc_final: 0.8266 (m-30) REVERT: C 88 HIS cc_start: 0.8011 (m90) cc_final: 0.7374 (m90) REVERT: C 120 SER cc_start: 0.9021 (m) cc_final: 0.8708 (p) outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.2345 time to fit residues: 97.4991 Evaluate side-chains 276 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 4.9990 chunk 69 optimal weight: 0.0980 chunk 89 optimal weight: 0.0770 chunk 68 optimal weight: 0.9980 chunk 102 optimal weight: 0.0030 chunk 121 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.3748 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN A 478 HIS A 569 GLN B 431 ASN ** B 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5942 moved from start: 0.7323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10482 Z= 0.187 Angle : 0.649 11.102 14277 Z= 0.333 Chirality : 0.045 0.150 1636 Planarity : 0.005 0.059 1792 Dihedral : 5.203 29.448 1382 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.93 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.23), residues: 1273 helix: 0.67 (0.35), residues: 222 sheet: -0.21 (0.24), residues: 455 loop : -0.67 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 644 HIS 0.004 0.001 HIS B 349 PHE 0.019 0.001 PHE B 793 TYR 0.018 0.001 TYR A 494 ARG 0.008 0.000 ARG D 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 ILE cc_start: 0.7555 (mp) cc_final: 0.7170 (tp) REVERT: A 372 GLU cc_start: 0.6115 (tm-30) cc_final: 0.5671 (tm-30) REVERT: A 419 ARG cc_start: 0.8293 (mmt-90) cc_final: 0.8012 (mmt-90) REVERT: A 426 ILE cc_start: 0.8057 (mm) cc_final: 0.7661 (tp) REVERT: A 464 TYR cc_start: 0.6646 (p90) cc_final: 0.5707 (p90) REVERT: A 480 THR cc_start: 0.6728 (m) cc_final: 0.6315 (m) REVERT: A 489 GLN cc_start: 0.7717 (mp10) cc_final: 0.7365 (mp10) REVERT: A 494 TYR cc_start: 0.6012 (m-80) cc_final: 0.5667 (m-80) REVERT: A 510 TRP cc_start: 0.7611 (p90) cc_final: 0.7039 (p90) REVERT: A 511 ILE cc_start: 0.8014 (tp) cc_final: 0.7740 (mm) REVERT: A 569 GLN cc_start: 0.6942 (tp-100) cc_final: 0.6607 (tp40) REVERT: A 577 LYS cc_start: 0.8240 (mptt) cc_final: 0.7937 (mptt) REVERT: A 605 TYR cc_start: 0.8035 (m-80) cc_final: 0.7750 (m-10) REVERT: A 655 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6532 (pp20) REVERT: A 725 PHE cc_start: 0.6577 (m-80) cc_final: 0.6284 (m-80) REVERT: A 753 ILE cc_start: 0.7917 (mm) cc_final: 0.7653 (tp) REVERT: A 767 TYR cc_start: 0.6821 (p90) cc_final: 0.6435 (p90) REVERT: A 821 LYS cc_start: 0.7453 (tttt) cc_final: 0.7048 (ttmt) REVERT: B 447 TRP cc_start: 0.6543 (p-90) cc_final: 0.6139 (p-90) REVERT: B 493 PHE cc_start: 0.7806 (m-80) cc_final: 0.7538 (m-80) REVERT: B 521 ASP cc_start: 0.6954 (p0) cc_final: 0.6472 (m-30) REVERT: B 582 LYS cc_start: 0.7581 (mmmt) cc_final: 0.7352 (mmmt) REVERT: B 647 MET cc_start: 0.6529 (mmm) cc_final: 0.4837 (tmm) REVERT: B 682 ARG cc_start: 0.7025 (tpt90) cc_final: 0.6307 (ttp80) REVERT: B 755 SER cc_start: 0.7781 (m) cc_final: 0.7282 (p) REVERT: B 761 ASP cc_start: 0.6288 (t0) cc_final: 0.6075 (p0) REVERT: B 771 GLU cc_start: 0.7494 (tm-30) cc_final: 0.7262 (tp30) REVERT: B 782 LYS cc_start: 0.7620 (mtmm) cc_final: 0.6947 (mtmm) REVERT: B 814 MET cc_start: 0.4564 (mpp) cc_final: 0.4303 (mpp) REVERT: B 819 LYS cc_start: 0.7257 (tmtt) cc_final: 0.6397 (mtpt) REVERT: C 13 LEU cc_start: 0.8449 (mt) cc_final: 0.8228 (mt) REVERT: C 39 LEU cc_start: 0.8265 (mm) cc_final: 0.8045 (pt) REVERT: C 54 MET cc_start: 0.8600 (mtm) cc_final: 0.8157 (mtt) REVERT: C 61 TYR cc_start: 0.8676 (m-80) cc_final: 0.8048 (m-80) REVERT: C 62 GLN cc_start: 0.8226 (tt0) cc_final: 0.7618 (tt0) REVERT: C 65 LEU cc_start: 0.8551 (mt) cc_final: 0.8328 (mt) REVERT: C 81 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7548 (mm-30) REVERT: C 84 ARG cc_start: 0.8503 (mtp180) cc_final: 0.7493 (ttm170) REVERT: C 85 ASP cc_start: 0.8603 (m-30) cc_final: 0.8243 (m-30) REVERT: C 86 LEU cc_start: 0.8772 (mm) cc_final: 0.8560 (mm) REVERT: C 88 HIS cc_start: 0.7965 (m90) cc_final: 0.7368 (m90) REVERT: C 120 SER cc_start: 0.8981 (m) cc_final: 0.8765 (p) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.2336 time to fit residues: 95.7887 Evaluate side-chains 269 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 60 optimal weight: 0.0070 chunk 11 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 116 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN ** B 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5985 moved from start: 0.7667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 10482 Z= 0.217 Angle : 0.683 16.149 14277 Z= 0.352 Chirality : 0.046 0.272 1636 Planarity : 0.005 0.085 1792 Dihedral : 5.315 26.288 1382 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.63 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.23), residues: 1273 helix: 0.51 (0.35), residues: 224 sheet: -0.26 (0.24), residues: 457 loop : -0.67 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 644 HIS 0.005 0.001 HIS B 349 PHE 0.021 0.002 PHE C 92 TYR 0.018 0.001 TYR B 405 ARG 0.014 0.001 ARG A 400 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 296 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 ILE cc_start: 0.7633 (mp) cc_final: 0.7214 (tp) REVERT: A 339 LEU cc_start: 0.7852 (mm) cc_final: 0.7380 (mm) REVERT: A 372 GLU cc_start: 0.6337 (tm-30) cc_final: 0.5944 (tm-30) REVERT: A 400 ARG cc_start: 0.7329 (ttm110) cc_final: 0.7077 (ttm110) REVERT: A 426 ILE cc_start: 0.8117 (mm) cc_final: 0.7678 (tp) REVERT: A 464 TYR cc_start: 0.6687 (p90) cc_final: 0.5863 (p90) REVERT: A 480 THR cc_start: 0.6824 (m) cc_final: 0.6373 (m) REVERT: A 493 PHE cc_start: 0.7885 (m-80) cc_final: 0.7524 (m-80) REVERT: A 498 PHE cc_start: 0.7113 (t80) cc_final: 0.6801 (t80) REVERT: A 510 TRP cc_start: 0.7539 (p90) cc_final: 0.7056 (p90) REVERT: A 511 ILE cc_start: 0.8080 (tp) cc_final: 0.7831 (tp) REVERT: A 569 GLN cc_start: 0.6732 (tp-100) cc_final: 0.6416 (tp40) REVERT: A 577 LYS cc_start: 0.8212 (mptt) cc_final: 0.7972 (mptt) REVERT: A 655 GLU cc_start: 0.7199 (mt-10) cc_final: 0.6588 (pp20) REVERT: A 725 PHE cc_start: 0.6609 (m-80) cc_final: 0.6343 (m-80) REVERT: A 753 ILE cc_start: 0.7936 (mm) cc_final: 0.7670 (tp) REVERT: A 767 TYR cc_start: 0.6878 (p90) cc_final: 0.6488 (p90) REVERT: B 447 TRP cc_start: 0.6504 (p-90) cc_final: 0.6288 (p-90) REVERT: B 493 PHE cc_start: 0.7830 (m-80) cc_final: 0.7465 (m-80) REVERT: B 512 ARG cc_start: 0.6557 (pmt-80) cc_final: 0.6244 (pmt-80) REVERT: B 521 ASP cc_start: 0.6966 (p0) cc_final: 0.6480 (m-30) REVERT: B 647 MET cc_start: 0.6546 (mmm) cc_final: 0.4866 (tmm) REVERT: B 698 ASN cc_start: 0.6518 (p0) cc_final: 0.6165 (t0) REVERT: B 733 MET cc_start: 0.5719 (ptm) cc_final: 0.4831 (tmm) REVERT: B 761 ASP cc_start: 0.5880 (t0) cc_final: 0.5359 (t70) REVERT: B 771 GLU cc_start: 0.7516 (tm-30) cc_final: 0.7291 (tp30) REVERT: B 782 LYS cc_start: 0.7545 (mtmm) cc_final: 0.6950 (mtmm) REVERT: B 814 MET cc_start: 0.4669 (mpp) cc_final: 0.4449 (mpp) REVERT: B 819 LYS cc_start: 0.7456 (tmtt) cc_final: 0.6397 (mtpt) REVERT: C 8 ASP cc_start: 0.8011 (p0) cc_final: 0.7777 (p0) REVERT: C 54 MET cc_start: 0.8600 (mtm) cc_final: 0.8200 (mtt) REVERT: C 61 TYR cc_start: 0.8657 (m-80) cc_final: 0.8077 (m-80) REVERT: C 62 GLN cc_start: 0.8282 (tt0) cc_final: 0.7588 (tt0) REVERT: C 65 LEU cc_start: 0.8623 (mt) cc_final: 0.8382 (mt) REVERT: C 81 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7500 (mm-30) REVERT: C 84 ARG cc_start: 0.8558 (mtp180) cc_final: 0.7590 (ttm170) REVERT: C 85 ASP cc_start: 0.8637 (m-30) cc_final: 0.8289 (m-30) REVERT: C 88 HIS cc_start: 0.7959 (m90) cc_final: 0.7281 (m90) REVERT: C 120 SER cc_start: 0.8953 (m) cc_final: 0.8710 (p) REVERT: D 160 GLN cc_start: 0.7505 (mm-40) cc_final: 0.7115 (mm-40) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.2292 time to fit residues: 93.1758 Evaluate side-chains 276 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 49 optimal weight: 0.0010 chunk 88 optimal weight: 0.0270 chunk 34 optimal weight: 5.9990 chunk 102 optimal weight: 0.5980 chunk 107 optimal weight: 0.8980 chunk 112 optimal weight: 0.4980 chunk 74 optimal weight: 0.6980 chunk 119 optimal weight: 10.0000 overall best weight: 0.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN A 478 HIS ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN ** B 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5945 moved from start: 0.7823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 10482 Z= 0.190 Angle : 0.674 15.334 14277 Z= 0.344 Chirality : 0.046 0.214 1636 Planarity : 0.005 0.085 1792 Dihedral : 5.146 26.075 1382 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.01 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.23), residues: 1273 helix: 0.68 (0.35), residues: 224 sheet: -0.21 (0.24), residues: 469 loop : -0.58 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 644 HIS 0.004 0.001 HIS B 478 PHE 0.021 0.001 PHE B 793 TYR 0.023 0.001 TYR A 605 ARG 0.012 0.001 ARG A 400 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 ILE cc_start: 0.7547 (mp) cc_final: 0.7182 (tp) REVERT: A 372 GLU cc_start: 0.6085 (tm-30) cc_final: 0.5884 (tm-30) REVERT: A 374 ILE cc_start: 0.7207 (mp) cc_final: 0.6984 (mp) REVERT: A 426 ILE cc_start: 0.8075 (mm) cc_final: 0.7655 (tp) REVERT: A 464 TYR cc_start: 0.6692 (p90) cc_final: 0.5861 (p90) REVERT: A 498 PHE cc_start: 0.7106 (t80) cc_final: 0.6721 (t80) REVERT: A 510 TRP cc_start: 0.7535 (p90) cc_final: 0.7014 (p90) REVERT: A 511 ILE cc_start: 0.8213 (tp) cc_final: 0.8004 (tp) REVERT: A 569 GLN cc_start: 0.6595 (tp-100) cc_final: 0.6315 (tp40) REVERT: A 577 LYS cc_start: 0.8146 (mptt) cc_final: 0.7927 (mptt) REVERT: A 655 GLU cc_start: 0.7241 (mt-10) cc_final: 0.6568 (pp20) REVERT: A 725 PHE cc_start: 0.6632 (m-80) cc_final: 0.6350 (m-80) REVERT: A 753 ILE cc_start: 0.7824 (mm) cc_final: 0.7558 (tp) REVERT: A 767 TYR cc_start: 0.6792 (p90) cc_final: 0.6455 (p90) REVERT: B 447 TRP cc_start: 0.6526 (p-90) cc_final: 0.6267 (p-90) REVERT: B 470 TYR cc_start: 0.8015 (m-10) cc_final: 0.7762 (m-10) REVERT: B 493 PHE cc_start: 0.7812 (m-80) cc_final: 0.7449 (m-80) REVERT: B 512 ARG cc_start: 0.6435 (pmt-80) cc_final: 0.6206 (pmt-80) REVERT: B 521 ASP cc_start: 0.6952 (p0) cc_final: 0.6498 (m-30) REVERT: B 638 MET cc_start: 0.5768 (ppp) cc_final: 0.5499 (ppp) REVERT: B 647 MET cc_start: 0.6574 (mmm) cc_final: 0.4848 (tmm) REVERT: B 682 ARG cc_start: 0.6979 (tpt90) cc_final: 0.6254 (ttp80) REVERT: B 698 ASN cc_start: 0.6328 (p0) cc_final: 0.6043 (t0) REVERT: B 733 MET cc_start: 0.5261 (ptm) cc_final: 0.4505 (tmm) REVERT: B 758 LEU cc_start: 0.7557 (pt) cc_final: 0.7351 (pp) REVERT: B 782 LYS cc_start: 0.7558 (mtmm) cc_final: 0.6903 (mtmm) REVERT: B 814 MET cc_start: 0.4568 (mpp) cc_final: 0.4335 (mpp) REVERT: B 819 LYS cc_start: 0.7381 (tmtt) cc_final: 0.6569 (mtpt) REVERT: C 54 MET cc_start: 0.8627 (mtm) cc_final: 0.8158 (mtt) REVERT: C 57 THR cc_start: 0.8393 (p) cc_final: 0.7858 (p) REVERT: C 61 TYR cc_start: 0.8586 (m-80) cc_final: 0.8011 (m-80) REVERT: C 62 GLN cc_start: 0.8224 (tt0) cc_final: 0.7594 (tt0) REVERT: C 81 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7565 (mm-30) REVERT: C 84 ARG cc_start: 0.8545 (mtp180) cc_final: 0.7582 (ttm170) REVERT: C 85 ASP cc_start: 0.8610 (m-30) cc_final: 0.8269 (m-30) REVERT: C 88 HIS cc_start: 0.7915 (m90) cc_final: 0.7241 (m90) REVERT: C 120 SER cc_start: 0.8988 (m) cc_final: 0.8602 (p) REVERT: D 160 GLN cc_start: 0.7518 (mm-40) cc_final: 0.7208 (mm-40) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.2265 time to fit residues: 91.8980 Evaluate side-chains 274 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 83 optimal weight: 0.2980 chunk 125 optimal weight: 3.9990 chunk 115 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 0.1980 chunk 79 optimal weight: 2.9990 chunk 106 optimal weight: 0.1980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5962 moved from start: 0.8004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 10482 Z= 0.191 Angle : 0.667 15.296 14277 Z= 0.340 Chirality : 0.046 0.204 1636 Planarity : 0.005 0.075 1792 Dihedral : 5.188 31.643 1382 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.40 % Favored : 95.52 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.23), residues: 1273 helix: 0.72 (0.35), residues: 224 sheet: -0.17 (0.25), residues: 445 loop : -0.70 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 447 HIS 0.004 0.001 HIS B 349 PHE 0.023 0.002 PHE A 561 TYR 0.019 0.001 TYR A 379 ARG 0.005 0.000 ARG B 682 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 ILE cc_start: 0.7619 (mp) cc_final: 0.7180 (tp) REVERT: A 372 GLU cc_start: 0.6263 (tm-30) cc_final: 0.6009 (tm-30) REVERT: A 426 ILE cc_start: 0.8064 (mm) cc_final: 0.7652 (tp) REVERT: A 464 TYR cc_start: 0.6674 (p90) cc_final: 0.6006 (p90) REVERT: A 493 PHE cc_start: 0.7918 (m-80) cc_final: 0.7400 (m-80) REVERT: A 498 PHE cc_start: 0.6980 (t80) cc_final: 0.6684 (t80) REVERT: A 510 TRP cc_start: 0.7543 (p90) cc_final: 0.7020 (p90) REVERT: A 511 ILE cc_start: 0.8148 (tp) cc_final: 0.7896 (mm) REVERT: A 557 GLU cc_start: 0.6869 (pm20) cc_final: 0.6487 (pm20) REVERT: A 569 GLN cc_start: 0.6506 (tp-100) cc_final: 0.6264 (tp40) REVERT: A 577 LYS cc_start: 0.8086 (mptt) cc_final: 0.7788 (mptt) REVERT: A 605 TYR cc_start: 0.8260 (m-80) cc_final: 0.7786 (m-10) REVERT: A 644 TRP cc_start: 0.7426 (t-100) cc_final: 0.5990 (t60) REVERT: A 655 GLU cc_start: 0.7198 (mt-10) cc_final: 0.6541 (pp20) REVERT: A 725 PHE cc_start: 0.6672 (m-80) cc_final: 0.6392 (m-80) REVERT: A 753 ILE cc_start: 0.7817 (mm) cc_final: 0.7547 (tp) REVERT: A 767 TYR cc_start: 0.6811 (p90) cc_final: 0.6506 (p90) REVERT: B 447 TRP cc_start: 0.6551 (p-90) cc_final: 0.6286 (p-90) REVERT: B 502 PHE cc_start: 0.6296 (m-80) cc_final: 0.5604 (m-80) REVERT: B 512 ARG cc_start: 0.6552 (pmt-80) cc_final: 0.6261 (pmt-80) REVERT: B 521 ASP cc_start: 0.6909 (p0) cc_final: 0.6478 (m-30) REVERT: B 591 SER cc_start: 0.8604 (p) cc_final: 0.8333 (p) REVERT: B 647 MET cc_start: 0.6509 (mmm) cc_final: 0.4866 (tmm) REVERT: B 698 ASN cc_start: 0.6335 (p0) cc_final: 0.6069 (t0) REVERT: B 701 PHE cc_start: 0.5781 (p90) cc_final: 0.5553 (p90) REVERT: B 733 MET cc_start: 0.5342 (ptm) cc_final: 0.4536 (tmm) REVERT: B 782 LYS cc_start: 0.7642 (mtmm) cc_final: 0.6971 (mtmm) REVERT: B 814 MET cc_start: 0.4558 (mpp) cc_final: 0.4321 (mpp) REVERT: B 819 LYS cc_start: 0.7436 (tmtt) cc_final: 0.6674 (mtpt) REVERT: C 54 MET cc_start: 0.8605 (mtm) cc_final: 0.8145 (mtt) REVERT: C 57 THR cc_start: 0.8375 (p) cc_final: 0.7857 (p) REVERT: C 61 TYR cc_start: 0.8586 (m-80) cc_final: 0.7969 (m-80) REVERT: C 62 GLN cc_start: 0.8318 (tt0) cc_final: 0.7619 (tt0) REVERT: C 65 LEU cc_start: 0.8531 (mt) cc_final: 0.8316 (mt) REVERT: C 81 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7584 (mm-30) REVERT: C 84 ARG cc_start: 0.8588 (mtp180) cc_final: 0.7625 (ttm170) REVERT: C 85 ASP cc_start: 0.8620 (m-30) cc_final: 0.8252 (m-30) REVERT: C 88 HIS cc_start: 0.7956 (m90) cc_final: 0.7294 (m90) REVERT: C 120 SER cc_start: 0.8975 (m) cc_final: 0.8601 (p) REVERT: D 160 GLN cc_start: 0.7601 (mm-40) cc_final: 0.7287 (mm-40) outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.2284 time to fit residues: 91.1274 Evaluate side-chains 278 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 1.9990 chunk 92 optimal weight: 0.0570 chunk 14 optimal weight: 0.4980 chunk 27 optimal weight: 0.0270 chunk 100 optimal weight: 0.5980 chunk 41 optimal weight: 7.9990 chunk 102 optimal weight: 0.0470 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.2454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN A 489 GLN B 431 ASN ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.167415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.132545 restraints weight = 32474.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.137005 restraints weight = 20106.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.139946 restraints weight = 14050.205| |-----------------------------------------------------------------------------| r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6156 moved from start: 0.8156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 10482 Z= 0.180 Angle : 0.661 14.811 14277 Z= 0.336 Chirality : 0.045 0.189 1636 Planarity : 0.005 0.072 1792 Dihedral : 5.026 27.301 1382 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.85 % Favored : 96.07 % Rotamer: Outliers : 0.08 % Allowed : 0.34 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.24), residues: 1273 helix: 0.85 (0.35), residues: 223 sheet: -0.07 (0.25), residues: 454 loop : -0.63 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 556 HIS 0.003 0.001 HIS B 685 PHE 0.021 0.001 PHE B 793 TYR 0.016 0.001 TYR A 379 ARG 0.016 0.001 ARG A 400 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2836.28 seconds wall clock time: 51 minutes 32.45 seconds (3092.45 seconds total)